Contacts of the strand formed by residues 48 - 55 (chain A) in PDB entry 3FKL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A PHE* 3.8 2.9 - - - -
43A ASP* 2.9 28.5 + - - +
46A THR* 3.2 34.6 + - + +
47A GLY* 1.3 81.5 - - - +
49A ARG* 1.3 68.5 + - - +
50A VAL* 4.2 5.8 - - + -
87A LEU* 4.2 19.7 - - + -
107A HIS* 3.9 31.0 - - + +
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Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA 3.4 9.0 - - - +
42A PHE* 4.7 12.7 - - + -
47A GLY 4.1 1.2 + - - +
48A LEU* 1.3 76.8 - - - +
50A VAL* 1.3 62.4 + - - +
107A HIS* 4.2 4.2 - - - -
108A LEU* 3.2 43.6 + - + +
160A GLU* 5.6 5.3 + - - -
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR* 3.9 22.2 - - + -
40A ALA* 3.4 4.7 - - - -
41A ALA* 2.9 47.6 + - + +
43A ASP* 4.0 22.4 - - + +
48A LEU* 4.0 7.6 - - + +
49A ARG* 1.3 79.9 - - - +
51A ALA* 1.3 59.4 - - - +
52A VAL* 4.1 3.1 - - + -
87A LEU* 3.8 20.0 - - + -
105A VAL* 3.7 20.4 - - + -
106A THR 3.3 14.4 - - - +
108A LEU* 3.6 8.6 - - - +
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A VAL* 3.9 12.1 - - + -
39A CYS 3.5 4.5 - - - -
50A VAL* 1.3 72.8 - - - +
52A VAL* 1.3 60.9 + - - +
53A LYS 4.1 0.4 - - - -
104A LEU 3.5 1.7 - - - +
105A VAL* 3.3 5.0 - - - -
106A THR* 2.8 41.7 + - - +
107A HIS 3.8 1.1 - - - +
108A LEU* 3.8 10.0 - - + +
361A FKL 3.6 41.4 - - + +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP* 3.3 26.5 - - + -
20A VAL* 4.9 3.1 - - + -
24A TYR* 4.8 8.7 - - + -
27A LEU* 5.2 3.6 - - + -
38A VAL* 4.3 2.2 - - - -
39A CYS* 2.7 45.4 + - + +
41A ALA* 4.3 12.1 - - + -
50A VAL* 4.1 17.3 - - + -
51A ALA* 1.3 77.4 - - - +
53A LYS* 1.3 60.4 + - - +
90A PHE* 4.2 8.7 - - + -
103A TYR* 4.2 17.9 - - + -
104A LEU 3.4 7.0 - - - +
105A VAL* 3.9 21.5 - - + -
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP* 4.4 0.2 - - - -
33A GLY* 4.2 0.4 - - - -
34A ALA* 2.7 43.7 + - - +
36A GLY* 4.1 14.6 - - - +
37A SER 3.4 12.6 - - - +
38A VAL* 4.0 16.4 - - + +
52A VAL* 1.3 72.8 - - - +
54A LYS* 1.3 65.2 + - - +
55A LEU* 3.8 13.9 + - + -
71A GLU* 2.5 30.4 + - - -
102A VAL 3.8 0.2 - - - +
103A TYR* 3.3 4.7 - - - -
104A LEU* 2.8 44.1 + - + +
361A FKL 3.6 36.9 - - + +
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Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A THR* 2.9 26.2 - - + +
17A ILE 2.8 27.9 + - - -
18A TRP* 3.6 35.1 - - + +
36A GLY* 3.4 18.2 - - - -
37A SER* 3.2 10.9 + - - +
53A LYS* 1.3 73.5 - - - +
55A LEU* 1.3 72.9 + - - +
56A SER* 3.4 1.6 + - - -
101A ASP* 3.7 23.7 + - + -
102A VAL 3.7 6.5 - - - +
103A TYR* 3.4 37.8 + - + +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA 4.0 2.2 - - - +
35A TYR* 3.5 18.6 - - + +
53A LYS* 3.8 21.7 + - - -
54A LYS* 1.3 83.9 - - - +
56A SER* 1.3 62.0 + - - +
57A ARG 3.6 2.6 + - - -
58A PRO* 3.8 20.1 - - + +
68A THR* 3.6 40.2 - - + +
71A GLU* 3.6 23.6 - - + +
101A ASP* 5.5 1.9 - - - +
102A VAL* 3.0 34.9 + - + +
104A LEU* 4.3 15.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il